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(1) Biological Molecules > 1.4 Proteins > Flashcards

1.4 Proteins Flashcards

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Organic Chemistry 101 flashcards
1
Q

Which monomers make up proteins?

A

Amino acids.

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2
Q

There are … amino acids found in proteins common to all living organisms.

A

20

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3
Q

What is the general structure of an amino acid?

A

A chiral carbon bonded to:
- an amine group (-NH2)
- a carboxylic acid group (-COOH)
- a hydrogen atom
- an R group (this is how each amino acid differs → determines its properties)
- central carbon

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4
Q

What is the bond between amino acids?

A

Peptide bond.

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5
Q

How is a peptide bond formed?

A

Peptide bonds are formed when the amine group of one amino acid binds with the carbonyl carbon of another amino acid.
- condensation reaction as a molecule of water is lost (OH from carbonyl carbon and H from amine group)

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6
Q

How is a peptide bond broken?

A

Hydrolysis reaction (addition of a water molecule).

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7
Q

Describe the primary structure of a protein.

A

The sequence of amino acids bonded by covalent peptide bonds.
- DNA determines the primary structure
- affects the shape and therefore the function of the protein
- structure is specific for each protein

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8
Q

Describe the secondary structure of a protein.

A

The secondary structure of a protein occurs when the weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds
- bonds can be broken by high temperatures and pH changes

2 shapes:
- α-helix
- β-pleated sheet

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9
Q

Describe the tertiary structure of a protein.

A

Further conformational change of the secondary structure leads to additional bonds forming between the R groups.

3 bonds:
- Hydrogen
- Disulphide
- Ionic

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10
Q

What is the role of hydrogen bonds in the structure of proteins.

A
  • form between strongly polar R groups
  • weakest
  • most common as they form across a wide variety of R groups
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11
Q

What is the role of ionic bonds in the structure of proteins.

A
  • form between positively charged (amine group -NH3+) and negatively charged (carboxylic acid -COOH-) R groups
  • stronger than hydrogen bonds but they are not common
  • bonds are broken by pH changes
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12
Q

What is the role of disulphide bridges in the structure of proteins.

A
  • form between two cysteine R groups
  • strongest within a protein, but occur less frequently, and help stabilise the proteins
  • can be broken by reduction
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13
Q

Describe the quaternary structure of a protein.

A

proteins that have more than one polypeptide chain

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14
Q

Describe the test for a protein.

A

Biuret Test
1. A few drops of biuret reagent is added
- liquid solution of sample is treated with NaOH or KOH (make it alkaline)
- add a few drops of copper(II) sulfate solution

+VE Result: colour change of blue → purple

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15
Q

What are 2 types of proteins?

A
  • globular
  • fibrous
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16
Q

Describe the structure of haemoglobin.

A
  • it has a quaternary structure four polypeptide chains
  • two α–globins and two β–globins
  • globular protein
  • four haem groups Fe2+
  • can bind to four oxygen molecules
17
Q

Describe the structure of collagen.

A
  • three polypeptide chains closely held together by hydrogen bonds to form a triple helix.
18
Q

What are enzymes?

A

Enzymes are biological catalysts. Structurally, they are globular proteins.

19
Q

What is the lock-and-key model?

A
  • Emil Fisher suggested that both enzymes and substrates were rigid structures that locked into each other very precisely (like a lock and key)
    1. Substrate fits exactly into the complementary active site
    2. This forms an enzyme-substrate complex
    3. Reaction takes place and an enzyme-product complex is formed
    4. Products are released
20
Q

What is the induced-fit model?

A
  • modified model
    1. The substrate does not fit the enzyme’s active site completely
    2. The enzyme and it’s active site can change shape slightly as the substrate molecule enters the enzyme (known as conformational changes) → ensures an ideal binding arrangement between the enzyme and substrate
    3. Forms an enzyme-substrate complex
    4. Reaction takes place and an enzyme-product complex is formed
    5. Products are released
21
Q

How do enzymes work?

A

Enzymes work by lowering the activation energy of a reaction and in doing so they provide an alternative energy pathway.

22
Q

Describe what is meant by enzyme specificity.

A

Enzyme active sites have a specific shape (determined by its tertiary structure) that is complementary to specific substrates.
- extremes of heat or pH can change the shape of the active site, preventing substrate binding → denaturation

23
Q

What determines the shape of an enzymes active site?

A

Its tertiary structure.

24
Q

Name the three types of peptidases and how they act.

A
  • dipeptidases (breaks the peptide bonds in dipeptides to form individual amino acids)
  • exopeptidases (breaks a peptide bond at the end of the polypeptide chain)
  • endopeptidases (breaks a peptide bond in the middle of the polypeptide chain)
25
Q

Limiting Factors Affecting Enzymes: Temperature

A
  • enzymes have a specific optimum temperature
  • lower temperatures either prevent reactions from proceeding or slow them down (low kinetic energy and low frequency of successful collisions)
  • high temperatures speed up the rate of reaction
  • when temperatures become too high the rate of reaction drops sharply as the enzyme begins to denature (hydrogen bonds break, change in tertiary structure, permanently damages the active site preventing enzyme-substrate complexes from forming)
26
Q

Limiting Factors Affecting Enzymes: pH

A
  • all enzymes have an optimum pH
  • enzymes are denatured at extremes of pH (below and above the optimum pH causes the hydrogen and ionic bonds to break which alters the shape of the active site)
27
Q

Limiting Factors Affecting Enzymes: Enzyme Concentration

A
  • the higher the enzyme concentration in a reaction mixture, the greater the number of active sites available and the greater the likelihood of enzyme-substrate complex formation
  • provided there is sufficient substrate available, the initial rate of reaction increases linearly with enzyme concentration
  • will not increase rate if substrate concentration becomes limiting
28
Q

Limiting Factors Affecting Enzymes: Substrate Concentration

A
  • the greater the substrate concentration, the higher the rate of reaction
  • as more successful collisions and therefore more kinetic energy= higher ROR
  • the likelihood of enzyme-substrate complex formation increases
  • will not increase rate when active site saturation is reached as the enzyme concentration becomes limiting
29
Q

Limiting Factors Affecting Enzymes: Inhibitors

A
  • both types of inhibitors slow down or stop enzyme activity
  • increasing the concentration of an inhibitor, therefore, reduces the rate of reaction and eventually, if inhibitor concentration continues to be increased, the reaction will stop completely
  • for competitive inhibitors, increasing the substrate concentration can increase the rate of reaction
30
Q

How does a competitive inhibitor work?

A
  • competitive inhibitors bind to the same active site as the complementary substrate as they have a similar shape.
  • this means it’s competes with the substrate for the same active site
    -occupies the active site, unbinds as no reaction occurs then the complmentary substrate binds
31
Q

How does a non-competitive inhibitor work?

A
  • non-competitive inhibitors bind to the enzyme at an allosteric site
  • this alters the shape of the active site
  • so substrate is no longer complementary therefore prevents the substrate from binding to it
  • increasing substrate concentration does not increase RoR as active site is no longer complementary
32
Q

Enzymes can be … (produced and function inside cells) or … (secreted by cells and catalyse reactions outside cells).

A

(1) intracellular
(2) extracellular

33
Q

Enzyme reactions can be catabolic meaning …

A

they involve the breakdown of complex molecules into simpler products
(e.g. cellular respiration and hydrolysis)

34
Q

Enzyme reactions can be anabolic meaning …

A

they involve the building up of more complex molecules from simpler ones
(e.g. protein synthesis and condensation)

(1) Biological Molecules (8 decks)

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